Calcium in PDB 9qdt: Cytochrome C Peroxidase Yhja

All present enzymatic activity of Cytochrome C Peroxidase Yhja:
1.11.1.5;

The structure of Cytochrome C Peroxidase Yhja, PDB code: 9qdt was solved by O.Einsle, A.Wuest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.15 / 2.57
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.42, 101.42, 134.68, 90, 90, 90
R / Rfree (%)	17.2 / 22.2

The structure of Cytochrome C Peroxidase Yhja also contains other interesting chemical elements:

Iron	(Fe)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Cytochrome C Peroxidase Yhja (pdb code 9qdt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cytochrome C Peroxidase Yhja, PDB code: 9qdt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cytochrome C Peroxidase Yhja


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cytochrome C Peroxidase Yhja within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:39.5 occ:1.00 O A:PRO412 2.4 34.7 1.0 O A:HOH621 2.4 28.9 1.0 OD1 A:ASN235 2.4 35.9 1.0 O A:HOH618 2.4 29.9 1.0 O A:HOH615 2.5 29.7 1.0 O A:THR410 2.5 29.4 1.0 CG A:ASN235 3.5 32.8 1.0 C A:PRO412 3.6 35.2 1.0 C A:THR410 3.7 30.2 1.0 ND2 A:ASN235 3.9 39.0 1.0 CA A:TYR413 4.2 33.5 1.0 O A:HOH624 4.3 40.9 1.0 CB A:THR410 4.3 31.4 1.0 N A:TYR413 4.3 32.0 1.0 O2A A:HEC502 4.3 37.9 1.0 C A:ALA411 4.4 31.5 1.0 O1A A:HEC502 4.4 37.6 1.0 OG1 A:THR410 4.4 34.7 1.0 N A:PRO412 4.5 31.9 1.0 O A:ALA236 4.5 33.6 1.0 CD1 A:TYR413 4.5 27.8 1.0 CA A:THR410 4.6 30.2 1.0 O A:ALA411 4.6 32.5 1.0 CA A:PRO412 4.6 32.3 1.0 N A:ALA411 4.6 30.4 1.0 CA A:ALA411 4.7 31.5 1.0 CB A:ASN235 4.7 31.8 1.0 CGA A:HEC502 4.8 37.8 1.0 C A:TYR413 4.9 33.6 1.0 CE1 A:TYR413 5.0 29.8 1.0

Calcium binding site 2 out of 2 in the Cytochrome C Peroxidase Yhja


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cytochrome C Peroxidase Yhja within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:71.5 occ:1.00 O A:ALA136 2.4 49.6 1.0 O A:THR131 2.6 26.6 1.0 O A:LEU133 2.6 23.0 1.0 C A:ALA136 3.4 39.5 1.0 O A:HOH645 3.5 48.4 1.0 C A:THR131 3.7 23.1 1.0 C A:LEU133 3.7 20.9 1.0 CA A:GLY137 3.9 42.7 1.0 N A:LEU133 4.1 18.8 1.0 N A:GLY137 4.1 42.5 1.0 C A:ALA132 4.1 16.7 1.0 N A:ALA136 4.3 26.4 1.0 CA A:ALA132 4.4 16.9 1.0 CA A:ALA136 4.5 30.4 1.0 N A:ALA132 4.5 21.1 1.0 CA A:LEU133 4.6 20.7 1.0 CA A:THR131 4.6 25.2 1.0 O A:ALA132 4.6 17.6 1.0 N A:HIS134 4.7 20.7 1.0 C A:HIS134 4.8 24.1 1.0 C A:GLY137 4.8 45.2 1.0 O A:HIS134 4.9 29.2 1.0 CA A:HIS134 4.9 23.1 1.0 N A:LYS138 4.9 48.6 1.0

P.Hewitt, J.Seidel, A.Wust, M.Smith, S.J.Maiocco, S.Shternberg, M.Hoffmann, T.Spatzal, S.Gerhardt, O.Einsle, S.J.Elliott. Escherichia Coli Triheme Enzyme Yhja: Structure and Reactivity. Biochemistry 2025.
ISSN: ISSN 0006-2960
PubMed: 40669070
DOI: 10.1021/ACS.BIOCHEM.5C00202